1
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Su C, Tuan NQ, Li WH, Cheng JH, Jin YY, Hong SK, Lee H, Qader M, Klein L, Shetye G, Pauli GF, Flanzblau SG, Cho SH, Zhao XQ, Suh JW. Enhancing rufomycin production by CRISPR/Cas9-based genome editing and promoter engineering in Streptomyces sp. MJM3502. Synth Syst Biotechnol 2025; 10:421-432. [PMID: 39925944 PMCID: PMC11803874 DOI: 10.1016/j.synbio.2025.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Revised: 12/31/2024] [Accepted: 01/07/2025] [Indexed: 02/11/2025] Open
Abstract
Streptomyces sp. MJM3502 is a promising producer of rufomycins, which are a class of potent anti-tuberculosis lead compounds. Although the structure, activity, and mechanism of the main rufomycin 4/6 and its analogs have been extensively studied, a significant gap remains in our understanding of the genome sequence and biosynthetic pathway of Streptomyces sp. MJM3502, and its metabolic engineering has not yet been reported. This study established the genetic manipulation platform for the strain. Using CRISPR/Cas9-based technology to in-frame insert the strong kasO∗p promoter upstream of the rufB and rufS genes of the rufomycin BGC, we increased rufomycin 4/6 production by 4.1-fold and 2.8-fold, respectively. Furthermore, designing recombinant strains by inserting the kasO∗p promoter upstream of the biosynthetic genes encoding cytochrome P450 enzymes led to new rufomycin derivatives. These findings provide the basis for enhancing the production of valuable natural compounds in Streptomyces and offer insights into the generation of novel active natural products via synthetic biology and metabolic engineering.
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Affiliation(s)
- Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Myongji Bioefficacy Research Center, Myongji University, Yongin, Gyeonggi-Do, 17058, Republic of Korea
| | - Nguyen-Quang Tuan
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi-Do, 17058, Republic of Korea
- R&D Center, Manbangbio Co. Ltd, Yongin, Gyeonggi-Do, 17058, Republic of Korea
| | - Wen-Hua Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Jin-Hua Cheng
- Myongji Bioefficacy Research Center, Myongji University, Yongin, Gyeonggi-Do, 17058, Republic of Korea
- Microbio Healthcare Co. Ltd, Yongin, Gyeonggi-Do, 17058, Republic of Korea
| | - Ying-Yu Jin
- R&D Center, Manbangbio Co. Ltd, Yongin, Gyeonggi-Do, 17058, Republic of Korea
| | - Soon-Kwang Hong
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi-Do, 17058, Republic of Korea
| | - Hyun Lee
- Institute for Tuberculosis Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, United States
| | - Mallique Qader
- Institute for Tuberculosis Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, United States
| | - Larry Klein
- Institute for Tuberculosis Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, United States
| | - Guido F. Pauli
- Institute for Tuberculosis Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, United States
| | - Scott G. Flanzblau
- Institute for Tuberculosis Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, United States
| | - Sang-Hyun Cho
- Institute for Tuberculosis Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Joo-Won Suh
- Myongji Bioefficacy Research Center, Myongji University, Yongin, Gyeonggi-Do, 17058, Republic of Korea
- Microbio Healthcare Co. Ltd, Yongin, Gyeonggi-Do, 17058, Republic of Korea
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2
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Zhou B, Shetye G, Klein LL, Wolf NM, Lee H, McAlpine JB, Harris G, Chen SN, Suh JW, Cho SH, Franzblau SG, Abad-Zapatero C, Pauli GF. Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues. JOURNAL OF NATURAL PRODUCTS 2025; 88:907-925. [PMID: 40126472 PMCID: PMC12038834 DOI: 10.1021/acs.jnatprod.4c01266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 03/05/2025] [Accepted: 03/07/2025] [Indexed: 03/25/2025]
Abstract
This study employed structural information from cocrystals of rufomycin 4 (1a) and caseinolytic protein C1 (ClpC1)-NTD-wt to guide design and semisynthesis of rufomycin analogues, evaluate their antituberculosis (TB) biological profiles, and establish structure-activity relationships (SAR). Covering three regions of interest (ROIs, A-C) as modification sites, 14 of the 30 semisynthetic analogues (2-31) showed similar or improved MICs relative to the main natural precursors, rufomycins 4/6 (1a/b). Compounds 5 and 27 exhibited up to 10-fold enhanced potency against Mycobacterium tuberculosis (Mtb) in vitro, with MIC values of 1.9 and 1.4 nM, respectively. Evaluation of ClpC1-binding properties used existing ClpC1-NTD complexes with rufomycin 4 (PDB: 6cn8) and ecumicin (PDB: 6pbs) as references. The newly reported X-ray ClpC1-NTD cocrystal structure of 11 (syn. But4-Cl) revealed significant conformational effects involving the side chains of certain amino acids of the heptapeptide and confirmed the importance of ROIs A-C for medicinal chemistry efforts. Observed interactions of the N-terminal tail of ClpC1 with the rufomycin analogues vs ecumicin explains their different modes of inactivating the ClpC1/P1/P2 homeostatic machinery. Collectively, the observations inform further SAR optimization strategies for the rufomycin class of antibiotics and complement our understanding of their mode of action.
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Affiliation(s)
- Bin Zhou
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Larry L. Klein
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Nina M. Wolf
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Hyun Lee
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Guy Harris
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Joo Won Suh
- Myongji
Bioefficacy Research Center, Myongji University, Myongji-Ro 116, Yongin, Gyeonggi-Do 17058, Republic of Korea
- Microbiohealthcare
Co., Ltd., Myongji-Ro
116, Yongin, Gyeonggi-Do 17058, Republic
of Korea
| | - Sang-Hyun Cho
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Celerino Abad-Zapatero
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Institute
for Tuberculosis Research, Pharmacognosy Institute, Center for Biomolecular
Sciences, andDepartment of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
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3
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Padva L, Gullick J, Coe LJ, Hansen MH, De Voss JJ, Crüsemann M, Cryle MJ. The Biarylitides: Understanding the Structure and Biosynthesis of a Fascinating Class of Cytochrome P450 Modified RiPP Natural Products. Chembiochem 2025; 26:e202400916. [PMID: 39714378 PMCID: PMC12002111 DOI: 10.1002/cbic.202400916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/19/2024] [Accepted: 12/20/2024] [Indexed: 12/24/2024]
Abstract
The biarylitides are a recently discovered class of RiPP natural products that are fascinating both from the small size of the core peptides as well as the diversity of peptide crosslinking exhibited by the cytochrome P450 enzymes found in these systems. In this review, we address the discovery and biosynthetic diversity of these systems and discuss the methods and challenges of analysing the structures of these constrained cyclic peptides. We also discuss the structures of the P450 enzymes involved in these pathways and address the potential for alternate catalytic outcomes and activities as seen most recently with the inclusion of biarylitide related enzymes within rufomycin biosynthesis.
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Affiliation(s)
- Leo Padva
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - Jemma Gullick
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Laura J. Coe
- School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQLD 4072Australia
| | - Mathias H. Hansen
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - James J. De Voss
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQLD 4072Australia
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
- Institute of Pharmaceutical BiologyGoethe University of Frankfurt60438FrankfurtGermany
| | - Max J. Cryle
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
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4
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Ding Y, Perez-Ortiz G, Butulan AG, Sharif H, Barry SM. Characterization of RufT Thioesterase Domain Reveals Insights into Rufomycin Cyclization and the Biosynthetic Origin of Rufomyazine. ACS Chem Biol 2025; 20:573-580. [PMID: 40048149 PMCID: PMC11934086 DOI: 10.1021/acschembio.4c00802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 02/20/2025] [Accepted: 02/25/2025] [Indexed: 03/22/2025]
Abstract
The nonribosomal cyclic peptides (NRcPs) rufomycins, produced by Streptomyces atratus, have attracted attention as antimycobacterials. Thus, there has been interest in engineering the corresponding biosynthetic pathway to produce novel derivatives. We have thus investigated the type I thioesterase (TE) of the NRPS RufT that catalyzes rufomycin peptide macrocyclization to understand its tolerance to changes in substrate peptide sequence. In contrast to our previously reported efficient cyclization chemistry, the recombinant RufT-TE domain and RufT-PCP-TE didomain, while tolerating some substrate structural changes, both produce high levels of hydrolyzed peptide. Closer analysis led to the identification of the natural product diketopiperazine rufomyazine in assays. The data indicate, with significant implications for rufomycin production, that RufT produces both cyclic and linear peptides. We propose that rufomyazine forms non-enzymatically from the linear peptide. In addition, it provides evidence for TE domains as gatekeepers in NRPS biosynthesis.
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Affiliation(s)
- Yaoyu Ding
- Department of Chemistry, Faculty of
Natural, Mathematical and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Gustavo Perez-Ortiz
- Department of Chemistry, Faculty of
Natural, Mathematical and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | | | | | - Sarah M. Barry
- Department of Chemistry, Faculty of
Natural, Mathematical and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
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5
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Massoni SC, Evans NJ, Hantke I, Fenton C, Torpey JH, Collins KM, Krysztofinska EM, Muench JH, Thapaliya A, Martínez-Lumbreras S, Hart Ferrell S, Slater C, Wang X, Fekade R, Obwar S, Yin S, Vazquez A, Prior CB, Turgay K, Isaacson RL, Camp AH. MdfA is a novel ClpC adaptor protein that functions in the developing Bacillus subtilis spore. Genes Dev 2025; 39:gad.352498.124. [PMID: 40086879 PMCID: PMC11960690 DOI: 10.1101/gad.352498.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Accepted: 02/13/2025] [Indexed: 03/16/2025]
Abstract
Bacterial protein degradation machinery consists of chaperone-protease complexes that play vital roles in bacterial growth and development and have sparked interest as novel antimicrobial targets. ClpC-ClpP (ClpCP) is one such chaperone-protease complex, recruited by adaptors to specific functions in the model bacterium Bacillus subtilis and other Gram-positive bacteria, including the pathogens Staphylococcus aureus and Mycobacterium tuberculosis Here we have identified a new ClpCP adaptor protein, MdfA (metabolic differentiation factor A; formerly YjbA), in a genetic screen for factors that help drive B. subtilis toward metabolic dormancy during spore formation. A knockout of mdfA stimulates gene expression in the developing spore, while aberrant expression of mdfA during vegetative growth is toxic. MdfA binds directly to ClpC to induce its oligomerization and ATPase activity, and this interaction is required for the in vivo effects of mdfA Finally, a cocrystal structure reveals that MdfA binds to the ClpC N-terminal domain at a location analogous to that on the M. tuberculosis ClpC1 protein where bactericidal cyclic peptides bind. Altogether, our data and that of an accompanying study by Riley and colleagues support a model in which MdfA induces ClpCP-mediated degradation of metabolic enzymes in the developing spore, helping drive it toward metabolic dormancy.
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Affiliation(s)
- Shawn C Massoni
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Nicola J Evans
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Ingo Hantke
- Institute for Microbiology, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Colleen Fenton
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - James H Torpey
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Katherine M Collins
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | | | - Janina H Muench
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Arjun Thapaliya
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | | | - Sé Hart Ferrell
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Celia Slater
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Xinyue Wang
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Ruth Fekade
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Sandra Obwar
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Siyu Yin
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Alishba Vazquez
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Christopher B Prior
- Department of Mathematical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Kürşad Turgay
- Institute for Microbiology, Leibniz Universität Hannover, Hannover 30419, Germany
- Max Planck Unit for the Science of Pathogens, Berlin 10117, Germany
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom;
| | - Amy H Camp
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA;
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6
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Süssmuth RD, Kulike‐Koczula M, Gao P, Kosol S. Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research. Angew Chem Int Ed Engl 2025; 64:e202414325. [PMID: 39611429 PMCID: PMC11878372 DOI: 10.1002/anie.202414325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 10/15/2024] [Accepted: 10/15/2024] [Indexed: 11/30/2024]
Abstract
In the fight against bacterial infections, particularly those caused by multi-resistant pathogens known as "superbugs", the need for new antibacterials is undoubted in scientific communities and is by now also widely perceived by the general population. However, the antibacterial research landscape has changed considerably over the past years. With few exceptions, the majority of big pharma companies has left the field and thus, the decline in R&D on antibacterials severely impacts the drug pipeline. In recent years, antibacterial research has increasingly relied on smaller companies or academic research institutions, which mostly have only limited financial resources, to carry a drug discovery and development process from the beginning and through to the beginning of clinical phases. This review formulates the requirements for an antibacterial in regard of targeted pathogens, resistance mechanisms and drug discovery. Strategies are shown for the discovery of new antibacterial structures originating from natural sources, by chemical synthesis and more recently from artificial intelligence approaches. This is complemented by principles for the computer-aided design of antibacterials and the refinement of a lead structure. The second part of the article comprises a compilation of antibacterial molecules classified according to bacterial target structures, e.g. cell wall synthesis, protein synthesis, as well as more recently emerging target classes, e.g. fatty acid synthesis, proteases and membrane proteins. Aspects of the origin, the antibacterial spectrum, resistance and the current development status of the presented drug molecules are highlighted.
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Affiliation(s)
- Roderich D. Süssmuth
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 124, TC210629BerlinGermany
| | - Marcel Kulike‐Koczula
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 124, TC210629BerlinGermany
| | - Peng Gao
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 124, TC210629BerlinGermany
| | - Simone Kosol
- Medical School BerlinDepartment Human MedicineRüdesheimer Strasse 5014195BerlinGermany
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7
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Weinhäupl K, Meuret L, Desrat S, Roussi F, Morellet N, Beaupierre S, Guillou C, van Heijenoort C, Abian O, Vega S, Wolf I, Akopian T, Krandor O, Rubin E, Velazquez-Campoy A, Gauto D, Fraga H. Identification of new ClpC1-NTD binders for Mycobacterium tuberculosis drug development. Sci Rep 2025; 15:4146. [PMID: 39900984 PMCID: PMC11791199 DOI: 10.1038/s41598-025-87535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 01/20/2025] [Indexed: 02/05/2025] Open
Abstract
MtbClpC1 is a promising drug target against tuberculosis. Recent studies have shown that several natural product antibiotics targeting the unfoldase N-terminal domain can impair MtbClpC1 function resulting in cell death. While the pharmacological properties of these natural product antibiotics prevent their use in the clinic, similar molecules binding to the same binding pockets can result in new drugs against Mtb. Here we demonstrate that we successfully used in silico screening to identify new ClpC1 N-terminal domain binders with micromolar affinity from a small compound library. In addition, we experimentally demonstrate that the new compounds bind to the same pockets used by the natural product antibiotics and inhibit ClpC1 function.
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Affiliation(s)
| | - Louis Meuret
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France
| | - Sandy Desrat
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France
| | - Fanny Roussi
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France
| | - Nelly Morellet
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France
| | - Sandra Beaupierre
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France
| | - Catherine Guillou
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France
| | - Olga Abian
- Institute for Health Research Aragon (IIS Aragon), Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI) & Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Ian Wolf
- Harvard School of Public Health, Boston, USA
| | | | | | - Eric Rubin
- Harvard School of Public Health, Boston, USA
| | - Adrian Velazquez-Campoy
- Institute for Health Research Aragon (IIS Aragon), Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI) & Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
| | - Diego Gauto
- Institut de Chimie des Substances Naturelles (ICSN), Centre national de la recherche scientifique (CNRS) , Gif-Sur-Yvette, France.
| | - Hugo Fraga
- Institute for Research and Innovation in HealthI3S, Porto, Portugal.
- Biochemistry Department, Medical Faculty, Porto University, Porto, Portugal.
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8
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Bedding MJ, Forster BC, Giltrap AM, Stevens MT, Corcilius L, Britton WJ, Payne RJ. Modular Total Synthesis and Antimycobacterial Activity of Rufomycins. Org Lett 2024; 26:10993-10998. [PMID: 39653016 DOI: 10.1021/acs.orglett.4c04163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
The rufomycins are a family of nonribosomal cyclic peptides isolated from the deep sea-dwelling Streptomyces atratus. Herein, we describe the total synthesis of six congeners in the rufomycin family. Synthesis was achieved through a modular solid-phase strategy, incorporating synthetic nonproteinogenic amino acids: l-2-amino-4-hexenoic acid, tert-prenyl-l-tryptophan (and related (S)-epoxide), and N-methyl-δ-hydroxy-l-leucine. Following macrolactamization, these peptides were further diversified through late-stage oxidation and secondary cyclization to furnish a library of six synthetic natural products. Rufomycins 4 and 22, bearing an unusual 6-hydroxypiperidin-2-one structural motif, exhibited impressive activity against the virulent H37Rv strain of Mycobacterium tuberculosis (MIC50 = 350-670 nM).
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Affiliation(s)
- Max J Bedding
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bryton C Forster
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Andrew M Giltrap
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Maxwell T Stevens
- Tuberculosis Research Program, Centenary Institute, and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Leo Corcilius
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Warwick J Britton
- Tuberculosis Research Program, Centenary Institute, and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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9
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Zhao P, Hou P, Zhang Z, Li X, Quan C, Xue Y, Lei K, Li J, Gao W, Fu F. Microbial-derived peptides with anti-mycobacterial potential. Eur J Med Chem 2024; 276:116687. [PMID: 39047606 DOI: 10.1016/j.ejmech.2024.116687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis, has become the leading cause of death. The subsequent emergence of multidrug-resistant, extensively drug-resistant and totally drug-resistant strains, brings an urgent need to discover novel anti-TB drugs. Among them, microbial-derived anti-mycobacterial peptides, including ribosomally synthesized and post-translationally modified peptides (RiPPs) and multimodular nonribosomal peptides (NRPs), now arise as promising candidates for TB treatment. This review presents 96 natural RiPP and NRP families from bacteria and fungi that have broad spectrum in vitro activities against non-resistant and drug-resistant mycobacteria. In addition, intracellular targets of 22 molecules are the subject of much attention. Meanwhile, chemical features of 38 families could be modified in order to improve properties. In final, structure-activity relationships suggest that the modifications of various groups, especially the peptide side chains, the amino acid moieties, the cyclic peptide skeletons, various special groups, stereochemistry and entire peptide chain length are important for increasing the potency.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Pu Hou
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Zhishen Zhang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xin Li
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, Yuncheng University, 044000, China.
| | - Chunshan Quan
- Department of Life Science, Dalian Nationalities University, Dalian, 116600, China.
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Kun Lei
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Fangfang Fu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
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10
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024; 41:1235-1263. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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11
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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12
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Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
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Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
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13
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Ding Y, Lambden E, Peate J, Picken LJ, Rees TW, Perez-Ortiz G, Newgas SA, Spicer LAR, Hicks T, Hess J, Ulmschneider MB, Müller MM, Barry SM. Rapid Peptide Cyclization Inspired by the Modular Logic of Nonribosomal Peptide Synthetases. J Am Chem Soc 2024; 146:16787-16801. [PMID: 38842580 PMCID: PMC11191687 DOI: 10.1021/jacs.4c04711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
Nonribosomal cyclic peptides (NRcPs) are structurally complex natural products and a vital pool of therapeutics, particularly antibiotics. Their structural diversity arises from the ability of the multidomain enzyme assembly lines, nonribosomal peptide synthetases (NRPSs), to utilize bespoke nonproteinogenic amino acids, modify the linear peptide during elongation, and catalyze an array of cyclization modes, e.g., head to tail, side chain to tail. The study and drug development of NRcPs are often limited by a lack of easy synthetic access to NRcPs and their analogues, with selective macrolactamization being a major bottleneck. Herein, we report a generally applicable chemical macrocyclization method of unprecedented speed and selectivity. Inspired by biosynthetic cyclization, it combines the deprotected linear biosynthetic precursor peptide sequence with a highly reactive C-terminus to produce NRcPs and analogues in minutes. The method was applied to several NRcPs of varying sequences, ring sizes, and cyclization modes including rufomycin, colistin, and gramicidin S with comparable success. We thus demonstrate that the linear order of modules in NRPS enzymes that determines peptide sequence encodes the key structural information to produce peptides conformationally biased toward macrocyclization. To fully exploit this conformational bias synthetically, a highly reactive C-terminal acyl azide is also required, alongside carefully balanced pH and solvent conditions. This allows for consistent, facile cyclization of exceptional speed, selectivity, and atom efficiency. This exciting macrolactamization method represents a new enabling technology for the biosynthetic study of NRcPs and their development as therapeutics.
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Affiliation(s)
- Yaoyu Ding
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Edward Lambden
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Jessica Peate
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Lewis J. Picken
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Thomas W. Rees
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Gustavo Perez-Ortiz
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Sophie A. Newgas
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Lucy A. R. Spicer
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Thomas Hicks
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Jeannine Hess
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Martin B. Ulmschneider
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Manuel M. Müller
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Sarah M. Barry
- Department
of Chemistry, Faculty of Natural, Mathematical, and Engineering Sciences, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
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14
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Junk L, Schmiedel VM, Guha S, Fischel K, Greb P, Vill K, Krisilia V, van Geelen L, Rumpel K, Kaur P, Krishnamurthy RV, Narayanan S, Shandil RK, Singh M, Kofink C, Mantoulidis A, Biber P, Gmaschitz G, Kazmaier U, Meinhart A, Leodolter J, Hoi D, Junker S, Morreale FE, Clausen T, Kalscheuer R, Weinstabl H, Boehmelt G. Homo-BacPROTAC-induced degradation of ClpC1 as a strategy against drug-resistant mycobacteria. Nat Commun 2024; 15:2005. [PMID: 38443338 PMCID: PMC10914731 DOI: 10.1038/s41467-024-46218-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Antimicrobial resistance is a global health threat that requires the development of new treatment concepts. These should not only overcome existing resistance but be designed to slow down the emergence of new resistance mechanisms. Targeted protein degradation, whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. We are extending this concept by developing proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mycobacterium tuberculosis (Mtb) BacPROTACs are derived from cyclomarins which, when dimerized, generate compounds that recruit and degrade ClpC1. The resulting Homo-BacPROTACs reduce levels of endogenous ClpC1 in Mycobacterium smegmatis and display minimum inhibitory concentrations in the low micro- to nanomolar range in mycobacterial strains, including multiple drug-resistant Mtb isolates. The compounds also kill Mtb residing in macrophages. Thus, Homo-BacPROTACs that degrade ClpC1 represent a different strategy for targeting Mtb and overcoming drug resistance.
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Affiliation(s)
- Lukas Junk
- Organic Chemistry I, Saarland University, Campus Building C4.2, 66123, Saarbrücken, Germany.
| | - Volker M Schmiedel
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Somraj Guha
- Organic Chemistry I, Saarland University, Campus Building C4.2, 66123, Saarbrücken, Germany
| | - Katharina Fischel
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Kristin Vill
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225, Düsseldorf, Germany
| | - Violetta Krisilia
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225, Düsseldorf, Germany
| | - Lasse van Geelen
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225, Düsseldorf, Germany
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Parvinder Kaur
- Foundation for Neglected Disease Research, Plot No. 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru, 561203, Karnataka, India
| | - Ramya V Krishnamurthy
- Foundation for Neglected Disease Research, Plot No. 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru, 561203, Karnataka, India
| | - Shridhar Narayanan
- Foundation for Neglected Disease Research, Plot No. 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru, 561203, Karnataka, India
| | - Radha Krishan Shandil
- Foundation for Neglected Disease Research, Plot No. 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru, 561203, Karnataka, India
| | - Mayas Singh
- Foundation for Neglected Disease Research, Plot No. 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru, 561203, Karnataka, India
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Andreas Mantoulidis
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Philipp Biber
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Gerhard Gmaschitz
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Uli Kazmaier
- Organic Chemistry I, Saarland University, Campus Building C4.2, 66123, Saarbrücken, Germany
| | - Anton Meinhart
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Julia Leodolter
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - David Hoi
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Sabryna Junker
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | | | - Tim Clausen
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Rainer Kalscheuer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225, Düsseldorf, Germany
| | - Harald Weinstabl
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria.
| | - Guido Boehmelt
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer-Gasse 5-11, 1121, Vienna, Austria.
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15
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Boshoff HI, Malhotra N, Barry CE, Oh S. The Antitubercular Activities of Natural Products with Fused-Nitrogen-Containing Heterocycles. Pharmaceuticals (Basel) 2024; 17:211. [PMID: 38399426 PMCID: PMC10892018 DOI: 10.3390/ph17020211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Tuberculosis (TB) is notorious as the leading cause of death worldwide due to a single infectious entity and its causative agent, Mycobacterium tuberculosis (Mtb), has been able to evolve resistance to all existing drugs in the treatment arsenal complicating disease management programs. In drug discovery efforts, natural products are important starting points in generating novel scaffolds that have evolved to specifically bind to vulnerable targets not only in pathogens such as Mtb, but also in mammalian targets associated with human diseases. Structural diversity is one of the most attractive features of natural products. This review provides a summary of fused-nitrogen-containing heterocycles found in the natural products reported in the literature that are known to have antitubercular activities. The structurally targeted natural products discussed in this review could provide a revealing insight into novel chemical aspects with novel biological functions for TB drug discovery efforts.
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Affiliation(s)
| | | | | | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (H.I.B.); (N.M.); (C.E.B.III)
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16
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Jagdev MK, Tompa DR, Ling LL, Peoples AJ, Dandapat J, Mohapatra C, Lewis K, Vasudevan D. Crystal structure of the N-terminal domain of MtClpC1 in complex with the anti-mycobacterial natural peptide Lassomycin. Int J Biol Macromol 2023; 253:126771. [PMID: 37683752 DOI: 10.1016/j.ijbiomac.2023.126771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/25/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Antibiotics form our frontline therapy against disease-causing bacteria. Unfortunately, antibiotic resistance is becoming more common, threatening a future where these medications can no longer cure infections. Furthermore, the emergence of multidrug-resistant (MDR), totally drug-resistant (TDR), and extensively drug-resistant (XDR) tuberculosis has increased the urgency of discovering new therapeutic leads with unique modes of action. Some natural peptides derived from actinomycetes, such as Cyclomarin A, Lassomycin, Rufomycin I, and Ecumicin, have potent and specific bactericidal activity against Mycobacterium tuberculosis, with the specificity owing to the fact that these peptides target the ClpC1 ATPase, an essential enzyme in mycobacteria, and inhibit/activate the proteolytic activity of the ClpC1/P1/P2 complex that participates in protein homeostasis. Here, we report the high-resolution crystal structure of the N-terminal domain of ClpC1 (ClpC1 NTD) in complex with Lassomycin, showing the specific binding mode of Lassomycin. In addition, the work also compares the Lassomycin complex structure with the previously known structures of ClpC1 NTD in complex with other natural peptides such as Cyclomarin A, Rufomycin I, and Ecumicin.
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Affiliation(s)
- Manas K Jagdev
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India; Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Dharma R Tompa
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India
| | - Losee L Ling
- NovoBiotic Pharmaceuticals, Cambridge, MA 02138, USA
| | | | - Jagneshwar Dandapat
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Chinmayee Mohapatra
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA.
| | - Dileep Vasudevan
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India; Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India.
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17
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Verma A, Naik B, Kumar V, Mishra S, Choudhary M, Khan JM, Gupta AK, Pandey P, Rustagi S, Kakati B, Gupta S. Revolutionizing Tuberculosis Treatment: Uncovering New Drugs and Breakthrough Inhibitors to Combat Drug-Resistant Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:2369-2385. [PMID: 37944023 DOI: 10.1021/acsinfecdis.3c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Tuberculosis (TB) is a global health threat that causes significant mortality. This review explores chemotherapeutics that target essential processes in Mycobacterium tuberculosis, such as DNA replication, protein synthesis, cell wall formation, energy metabolism, and proteolysis. We emphasize the need for new drugs to treat drug-resistant strains and shorten the treatment duration. Emerging targets and promising inhibitors were identified by examining the intricate biology of TB. This review provides an overview of recent developments in the search for anti-TB drugs with a focus on newly validated targets and inhibitors. We aimed to contribute to efforts to combat TB and improve therapeutic outcomes.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Sadhna Mishra
- Faculty of Agricultural Sciences, GLA University, Mathura 281406, UP, India
| | - Megha Choudhary
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Arun Kumar Gupta
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchur 788011, Assam, India
| | - Sarvesh Rustagi
- Department of Food Technology, UCALS, Uttaranchal University, Dehradun 248007, Uttarakhand, India
| | - Barnali Kakati
- Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, U.K., India
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
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18
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Petkov R, Camp AH, Isaacson RL, Torpey JH. Targeting bacterial degradation machinery as an antibacterial strategy. Biochem J 2023; 480:1719-1731. [PMID: 37916895 PMCID: PMC10657178 DOI: 10.1042/bcj20230191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 11/03/2023]
Abstract
The exploitation of a cell's natural degradation machinery for therapeutic purposes is an exciting research area in its infancy with respect to bacteria. Here, we review current strategies targeting the ClpCP system, which is a proteolytic degradation complex essential in the biology of many bacterial species of scientific interest. Strategies include using natural product antibiotics or acyldepsipeptides to initiate the up- or down-regulation of ClpCP activity. We also examine exciting recent forays into BacPROTACs to trigger the degradation of specific proteins of interest through the hijacking of the ClpCP machinery. These strategies represent an important emerging avenue for combatting antimicrobial resistance.
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Affiliation(s)
- Radoslav Petkov
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Amy H. Camp
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, Massachusetts 01075, U.S.A
| | - Rivka L. Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - James H. Torpey
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
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19
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Wang W, Gu L, Wang J, Hu X, Wei B, Zhang H, Wang H, Chen J. Recent Advances in Polypeptide Antibiotics Derived from Marine Microorganisms. Mar Drugs 2023; 21:547. [PMID: 37888482 PMCID: PMC10608164 DOI: 10.3390/md21100547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
In the post-antibiotic era, the rapid development of antibiotic resistance and the shortage of available antibiotics are triggering a new health-care crisis. The discovery of novel and potent antibiotics to extend the antibiotic pipeline is urgent. Small-molecule antimicrobial peptides have a wide variety of antimicrobial spectra and multiple innovative antimicrobial mechanisms due to their rich structural diversity. Consequently, they have become a new research hotspot and are considered to be promising candidates for next-generation antibiotics. Therefore, we have compiled a collection of small-molecule antimicrobial peptides derived from marine microorganisms from the last fifteen years to show the recent advances in this field. We categorize these compounds into three classes-cyclic oligopeptides, cyclic depsipeptides, and cyclic lipopeptides-according to their structural features, and present their sources, structures, and antimicrobial spectrums, with a discussion of the structure activity relationships and mechanisms of action of some compounds.
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Affiliation(s)
| | | | | | | | | | | | - Hong Wang
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education & Key Laboratory Pharmaceutical Engineering of Zhejiang Province & College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianwei Chen
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education & Key Laboratory Pharmaceutical Engineering of Zhejiang Province & College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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20
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Ogbonna EC, Anderson HR, Beardslee PC, Bheemreddy P, Schmitz KR. Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1. Microbiol Spectr 2023; 11:e0454822. [PMID: 37341639 PMCID: PMC10433963 DOI: 10.1128/spectrum.04548-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/31/2023] [Indexed: 06/22/2023] Open
Abstract
The prevalence of drug-resistant Mycobacterium tuberculosis infections has prompted extensive efforts to exploit new drug targets in this globally important pathogen. ClpC1, the unfoldase component of the essential ClpC1P1P2 protease, has emerged as one particularly promising antibacterial target. However, efforts to identify and characterize compounds that impinge on ClpC1 activity are constrained by our limited knowledge of Clp protease function and regulation. To expand our understanding of ClpC1 physiology, we employed a coimmunoprecipitation and mass spectrometry workflow to identify proteins that interact with ClpC1 in Mycolicibacterium smegmatis, a surrogate for M. tuberculosis. We identify a diverse panel of interaction partners, many of which coimmunoprecipitate with both the regulatory N-terminal domain and the ATPase core of ClpC1. Notably, our interactome analysis establishes MSMEI_3879, a truncated gene product unique to M. smegmatis, as a novel proteolytic substrate. Degradation of MSMEI_3879 by ClpC1P1P2 in vitro requires exposure of its N-terminal sequence, reinforcing the idea that ClpC1 selectively recognizes disordered motifs on substrates. Fluorescent substrates incorporating MSMEI_3879 may be useful in screening for novel ClpC1-targeting antibiotics to help address the challenge of M. tuberculosis drug resistance. IMPORTANCE Drug-resistant tuberculosis infections are a major challenge to global public health. Much effort has been invested in identifying new drug targets in the causative pathogen, Mycobacterium tuberculosis. One such target is the ClpC1 unfoldase. Compounds have been identified that kill M. tuberculosis by disrupting ClpC1 activity, yet the physiological function of ClpC1 in cells has remained poorly defined. Here, we identify interaction partners of ClpC1 in a model mycobacterium. By building a broader understanding of the role of this prospective drug target, we can more effectively develop compounds that inhibit its essential cellular activities.
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Affiliation(s)
- Emmanuel C. Ogbonna
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Henry R. Anderson
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Patrick C. Beardslee
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Priyanka Bheemreddy
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Karl R. Schmitz
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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21
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Jordan S, Li B, Traore E, Wu Y, Usai R, Liu A, Xie ZR, Wang Y. Structural and spectroscopic characterization of RufO indicates a new biological role in rufomycin biosynthesis. J Biol Chem 2023; 299:105049. [PMID: 37451485 PMCID: PMC10424215 DOI: 10.1016/j.jbc.2023.105049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
Rufomycins constitute a class of cyclic heptapeptides isolated from actinomycetes. They are secondary metabolites that show promising treatment against Mycobacterium tuberculosis infections by inhibiting a novel drug target. Several nonproteinogenic amino acids are integrated into rufomycins, including a conserved 3-nitro-tyrosine. RufO, a cytochrome P450 (CYP)-like enzyme, was proposed to catalyze the formation of 3-nitro-tyrosine in the presence of O2 and NO. To define its biological function, the interaction between RufO and the proposed substrate tyrosine is investigated using various spectroscopic methods that are sensitive to the structural change of a heme center. However, a low- to high-spin state transition and a dramatic increase in the redox potential that are commonly found in CYPs upon ligand binding have not been observed. Furthermore, a 1.89-Å crystal structure of RufO shows that the enzyme has flexible surface regions, a wide-open substrate access tunnel, and the heme center is largely exposed to solvent. Comparison with a closely related nitrating CYP reveals a spacious and hydrophobic distal pocket in RufO, which is incapable of stabilizing a free amino acid. Molecular docking validates the experimental data and proposes a possible substrate. Collectively, our results disfavor tyrosine as the substrate of RufO and point to the possibility that the nitration occurs during or after the assembly of the peptides. This study indicates a new function of the unique nitrating enzyme and provides insights into the biosynthesis of nonribosomal peptides.
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Affiliation(s)
- Stephanie Jordan
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Bingnan Li
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Ephrahime Traore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Yifei Wu
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Remigio Usai
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Zhong-Ru Xie
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, Georgia, USA.
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22
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Jacobo-Delgado YM, Rodríguez-Carlos A, Serrano CJ, Rivas-Santiago B. Mycobacterium tuberculosis cell-wall and antimicrobial peptides: a mission impossible? Front Immunol 2023; 14:1194923. [PMID: 37266428 PMCID: PMC10230078 DOI: 10.3389/fimmu.2023.1194923] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most important infectious agents worldwide and causes more than 1.5 million deaths annually. To make matters worse, the drug resistance among Mtb strains has risen substantially in the last few decades. Nowadays, it is not uncommon to find patients infected with Mtb strains that are virtually resistant to all antibiotics, which has led to the urgent search for new molecules and therapies. Over previous decades, several studies have demonstrated the efficiency of antimicrobial peptides to eliminate even multidrug-resistant bacteria, making them outstanding candidates to counterattack this growing health problem. Nevertheless, the complexity of the Mtb cell wall makes us wonder whether antimicrobial peptides can effectively kill this persistent Mycobacterium. In the present review, we explore the complexity of the Mtb cell wall and analyze the effectiveness of antimicrobial peptides to eliminate the bacilli.
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23
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Taylor G, Cui H, Leodolter J, Giese C, Weber-Ban E. ClpC2 protects mycobacteria against a natural antibiotic targeting ClpC1-dependent protein degradation. Commun Biol 2023; 6:301. [PMID: 36944713 PMCID: PMC10030653 DOI: 10.1038/s42003-023-04658-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Mycobacterium tuberculosis Clp proteases are targeted by several antitubercular compounds, including cyclomarin A (CymA). CymA exerts its toxicity by binding to AAA + chaperone ClpC1. Here, we show that CymA can also bind a partial homologue of ClpC1, known as ClpC2, and we reveal the molecular basis of these interactions by determining the structure of the M. tuberculosis ClpC2:CymA complex. Furthermore, we show deletion of clpC2 in Mycobacterium smegmatis increases sensitivity to CymA. We find CymA exposure leads to a considerable upregulation of ClpC2 via a mechanism in which binding of CymA to ClpC2 prevents binding of ClpC2 to its own promoter, resulting in upregulation of its own transcription in response to CymA. Our study reveals that ClpC2 not only senses CymA, but that through this interaction it can act as a molecular sponge to counteract the toxic effects of CymA and possibly other toxins targeting essential protease component ClpC1 in mycobacteria.
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Affiliation(s)
- Gabrielle Taylor
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
| | - Hengjun Cui
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
| | - Julia Leodolter
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Christoph Giese
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland.
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24
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Xu X, Zhang L, Yang T, Qiu Z, Bai L, Luo Y. Targeting caseinolytic protease P and its AAA1 chaperone for tuberculosis treatment. Drug Discov Today 2023; 28:103508. [PMID: 36706830 DOI: 10.1016/j.drudis.2023.103508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
Caseinolytic protease P with its AAA1 chaperone, known as Mycobacterium tuberculosis (Mtb)ClpP1P2 proteolytic machinery, maintains protein homeostasis in Mtb cells and is essential for bacterial survival. It is regarded as an important biological target with the potential to address the increasingly serious issue of multidrug-resistant (MDR) TB. Over the past 10 years, many MtbClpP1P2-targeted modulators have been identified and characterized, some of which have shown potent anti-TB activity. In this review, we describe current understanding of the substrates, structure and function of MtbClpP1P2, classify the modulators of this important protein machine into several categories based on their binding subunits or pockets, and discuss their binding details; Such information provides insights for use in candidate drug research and development of TB treatments by targeting MtbClpP1P2 proteolytic machinery.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Qiu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lang Bai
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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25
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Bhanot A, Lunge A, Kumar N, Kidwai S, Singh R, Sundriyal S, Agarwal N. Discovery of small molecule inhibitors of Mycobacterium tuberculosis ClpC1: SAR studies and antimycobacterial evaluation. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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26
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Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action. J Biol Chem 2022; 298:102553. [PMID: 36208775 PMCID: PMC9661721 DOI: 10.1016/j.jbc.2022.102553] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/13/2022] Open
Abstract
The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural product antibiotics: cyclomarin, ecumicin, lassomycin, and rufomycin. Although these molecules are promising starting points for drug development, their mechanisms of action remain largely unknown. Taking advantage of a middle domain mutant, we determined the first structure of Mycobacterium tuberculosis ClpC1 in its apo, cyclomarin-, and ecumicin-bound states via cryo-EM. The obtained structure displays features observed in other members of the AAA+ family and provides a map for further drug development. While the apo and cyclomarin-bound structures are indistinguishable and have N-terminal domains that are invisible in their respective EM maps, around half of the ecumicin-bound ClpC1 particles display three of their six N-terminal domains in an extended conformation. Our structural observations suggest a mechanism where ecumicin functions by mimicking substrate binding, leading to ATPase activation and changes in protein degradation profile.
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27
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Ogbonna EC, Anderson HR, Schmitz KR. Identification of Arginine Phosphorylation in Mycolicibacterium smegmatis. Microbiol Spectr 2022; 10:e0204222. [PMID: 36214676 PMCID: PMC9604228 DOI: 10.1128/spectrum.02042-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/19/2022] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis is a leading cause of worldwide infectious mortality. The prevalence of multidrug-resistant Mycobacterium tuberculosis infections drives an urgent need to exploit new drug targets. One such target is the ATP-dependent protease ClpC1P1P2, which is strictly essential for viability. However, few proteolytic substrates of mycobacterial ClpC1P1P2 have been identified to date. Recent studies in Bacillus subtilis have shown that the orthologous ClpCP protease recognizes proteolytic substrates bearing posttranslational arginine phosphorylation. While several lines of evidence suggest that ClpC1P1P2 is similarly capable of recognizing phosphoarginine-bearing proteins, the existence of phosphoarginine modifications in mycobacteria has remained in question. Here, we confirm the presence of posttranslational phosphoarginine modifications in Mycolicibacterium smegmatis, a nonpathogenic surrogate of M. tuberculosis. Using a phosphopeptide enrichment workflow coupled with shotgun phosphoproteomics, we identified arginine phosphosites on several functionally diverse targets within the M. smegmatis proteome. Interestingly, phosphoarginine modifications are not upregulated by heat stress, suggesting divergent roles in mycobacteria and Bacillus. Our findings provide new evidence supporting the existence of phosphoarginine-mediated proteolysis by ClpC1P1P2 in mycobacteria and other actinobacterial species. IMPORTANCE Mycobacteria that cause tuberculosis infections employ proteolytic pathways that modulate cellular behavior by destroying specific proteins in a highly regulated manner. Some proteolytic enzymes have emerged as novel antibacterial targets against drug-resistant tuberculosis infections. However, we have only a limited understanding of how these enzymes function in the cell and how they select proteins for destruction. Some proteolytic enzymes are capable of recognizing proteins that carry an unusual chemical modification, arginine phosphorylation. Here, we confirm the existence of arginine phosphorylation in mycobacterial proteins. Our work expands our understanding of a promising drug target in an important global pathogen.
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Affiliation(s)
- Emmanuel C. Ogbonna
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Henry R. Anderson
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Karl R. Schmitz
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware, USA
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28
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Zhou B, Shetye G, Wolf NM, Chen SN, Qader M, Ray GJ, Lankin DC, Cho S, Cheng J, Suh JW, Franzblau SG, McAlpine JB, Pauli GF. New Rufomycins from Streptomyces atratus MJM3502 Expand Anti- Mycobacterium tuberculosis Structure-Activity Relationships. Org Lett 2022; 24:7265-7270. [PMID: 36194676 PMCID: PMC9588618 DOI: 10.1021/acs.orglett.2c02493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Four new rufomycins, compounds 1-4, named rufomycins 56, 57, 58, and 61, respectively, exhibiting new skeletal features, were obtained from Streptomyces atratus strain MJM3502 and were fully characterized. Compounds 1 and 2 possess a 4-imidazolidinone ring not previously encountered in this family of cyclopeptides, thereby resulting in a [5,17] bicyclic framework. The in vitro anti-Mycobacterium tuberculosis potency of compounds 3 and 4 is remarkable, with minimum inhibitory concentration values of 8.5 and 130 nM, respectively.
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Affiliation(s)
- Bin Zhou
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Nina M. Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Mallique Qader
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - G. Joseph Ray
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - David C. Lankin
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jinhua Cheng
- Myongji Bioefficacy Research Center, Myongji University, 116 Myongji-ro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Joo-Won Suh
- Myongji Bioefficacy Research Center, Myongji University, 116 Myongji-ro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Scott G. Franzblau
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
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29
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Motiwala T, Mthethwa Q, Achilonu I, Khoza T. ESKAPE Pathogens: Looking at Clp ATPases as Potential Drug Targets. Antibiotics (Basel) 2022; 11:1218. [PMID: 36139999 PMCID: PMC9495089 DOI: 10.3390/antibiotics11091218] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Bacterial antibiotic resistance is rapidly growing globally and poses a severe health threat as the number of multidrug resistant (MDR) and extensively drug-resistant (XDR) bacteria increases. The observed resistance is partially due to natural evolution and to a large extent is attributed to antibiotic misuse and overuse. As the rate of antibiotic resistance increases, it is crucial to develop new drugs to address the emergence of MDR and XDR pathogens. A variety of strategies are employed to address issues pertaining to bacterial antibiotic resistance and these strategies include: (1) the anti-virulence approach, which ultimately targets virulence factors instead of killing the bacterium, (2) employing antimicrobial peptides that target key proteins for bacterial survival and, (3) phage therapy, which uses bacteriophages to treat infectious diseases. In this review, we take a renewed look at a group of ESKAPE pathogens which are known to cause nosocomial infections and are able to escape the bactericidal actions of antibiotics by reducing the efficacy of several known antibiotics. We discuss previously observed escape mechanisms and new possible therapeutic measures to combat these pathogens and further suggest caseinolytic proteins (Clp) as possible therapeutic targets to combat ESKAPE pathogens. These proteins have displayed unmatched significance in bacterial growth, viability and virulence upon chronic infection and under stressful conditions. Furthermore, several studies have showed promising results with targeting Clp proteins in bacterial species, such as Mycobacterium tuberculosis, Staphylococcus aureus and Bacillus subtilis.
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Affiliation(s)
- Tehrim Motiwala
- Discipline of Biochemistry, School of Life Sciences, University of Kwa-Zulu Natal-Pietermaritzburg Campus, Scottsville 3209, South Africa
| | - Qiniso Mthethwa
- Discipline of Biochemistry, School of Life Sciences, University of Kwa-Zulu Natal-Pietermaritzburg Campus, Scottsville 3209, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Thandeka Khoza
- Discipline of Biochemistry, School of Life Sciences, University of Kwa-Zulu Natal-Pietermaritzburg Campus, Scottsville 3209, South Africa
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30
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Screening of Microbial Fermentation Products for Anti-M. tuberculosis Activity. Animals (Basel) 2022; 12:ani12151947. [PMID: 35953936 PMCID: PMC9367595 DOI: 10.3390/ani12151947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/19/2022] Open
Abstract
Simple Summary M. tuberculosis (M.tb) is the main pathogen of tuberculosis (TB). The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) M.tb has brought new challenges to the treatment of TB. Therefore, finding new materials for the development of natural anti-TB drugs is crucial to the prevention and treatment of TB. In order to discover new anti-TB drug materials, we isolated microorganisms from the soil and tested the anti-M.tb activity of their fermentation products. The results showed that the four fermentation products had anti-M.tb activities in vitro and in intracellular bacteria. The qPCR results showed that the four fermentation products down-regulated some growth-essential gene expression of M.tb. Thus, we speculated that the fermentation product may exert its anti-M.tb effect by down-regulating the expression of the essential genes of M.tb. Abstract Tuberculosis (TB), caused by M. tuberculosis (M.tb), is the leading infectious cause of mortality worldwide. The emergence of drug-resistant M.tb has made the control of TB more difficult. In our study, we investigated the ability of microorganism fermentation products from the soil to inhibit M.tb. We successfully identified four fermentation products (Micromonospora chokoriensis, Micromonospora purpureochromogenes, Micromonospora profundi, Streptomyces flavofungini) that inhibited the growth of M.tb in vitro and in intracellular bacteria at 25 μg/mL MIC. Importantly, the fermentation products decreased some essential gene expression levels for M.tb growth. Our data provide the possibility that microbial fermentation products have potential development value for anti-M.tb drugs.
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Taylor G, Frommherz Y, Katikaridis P, Layer D, Sinning I, Carroni M, Weber-Ban E, Mogk A. Antibacterial peptide CyclomarinA creates toxicity by deregulating the Mycobacterium tuberculosis ClpC1/ClpP1P2 protease. J Biol Chem 2022; 298:102202. [PMID: 35768046 PMCID: PMC9305358 DOI: 10.1016/j.jbc.2022.102202] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
The ring-forming AAA+ hexamer ClpC1 associates with the peptidase ClpP1P2 to form a central, ATP-driven protease in Mycobacterium tuberculosis (Mtb). ClpC1 is essential for Mtb viability and has been identified as the target of antibacterial peptides like CyclomarinA (CymA) that exhibit strong toxicity towards Mtb. The mechanistic actions of these drugs are poorly understood, but seem diverse, as they have different effects on ClpC1's ATPase and proteolytic activities. Here, we dissected how ClpC1 activity is controlled and how this control is deregulated by CymA. We show that ClpC1 exists in diverse activity states correlating with its assembly. The basal activity of ClpC1 is low, as it predominantly exists in an inactive, non-hexameric resting state. We show CymA stimulates ClpC1 activity by promoting formation of super-complexes composed of multiple ClpC1 hexameric rings, enhancing ClpC1/ClpP1P2 degradation activity towards a diverse range of substrates. Both the ClpC1 resting state and the CymA-induced alternative assembly state rely on interactions between the ClpC1 coiled-coil middle domains (MDs). Accordingly, we found mutation of the conserved aromatic F444 residue located at the MD tip blocks MD interactions and prevents assembly into higher order complexes, thereby leading to constitutive ClpC1 hexamer formation. We demonstrate this assembly state exhibits the highest ATPase and proteolytic activities, yet its heterologous expression in Escherichia coli is toxic, indicating that the formation of such a state must be tightly controlled. Taken together, these findings define the basis of control of ClpC1 activity and show how ClpC1 overactivation by an antibacterial drug generates toxicity.
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Affiliation(s)
- Gabrielle Taylor
- ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Yannick Frommherz
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Division of Chaperones and Proteases, Division of Chaperones and Proteases, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Panagiotis Katikaridis
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Division of Chaperones and Proteases, Division of Chaperones and Proteases, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Dominik Layer
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Marta Carroni
- Swedish Cryo-EM Facility, Science for Life Laboratory Stockholm University, Solna, Sweden
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland.
| | - Axel Mogk
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Division of Chaperones and Proteases, Division of Chaperones and Proteases, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.
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32
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Addison W, Frederickson M, Coyne AG, Abell C. Potential therapeutic targets from Mycobacterium abscessus ( Mab): recently reported efforts towards the discovery of novel antibacterial agents to treat Mab infections. RSC Med Chem 2022; 13:392-404. [PMID: 35647542 PMCID: PMC9020770 DOI: 10.1039/d1md00359c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/09/2022] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium abscessus (Mab) are rapidly growing mycobacteria that cause severe and persistent infections in both skin and lung tissues. Treatment regimens involve the extended usage of complex combinations of drugs, often leading to severe adverse side effects, particularly in immunocompromised patients. Current macrolide therapies are gradually proving to be less effective, largely due to emergence of antibiotic resistance; there is therefore an increasing need for the discovery of new antibacterials that are active against Mab. This review highlights recent research centred upon a number of potential therapeutic targets from Mab (Ag85C, ClpC1, GyrB, MmpL3 and TrmD), and discusses the various approaches used to discover small molecule inhibitors, in the search for future antibiotics for the treatment of Mab infections.
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Affiliation(s)
- William Addison
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Martyn Frederickson
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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33
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Mabanglo MF, Houry WA. Recent structural insights into the mechanism of ClpP protease regulation by AAA+ chaperones and small molecules. J Biol Chem 2022; 298:101781. [PMID: 35245501 PMCID: PMC9035409 DOI: 10.1016/j.jbc.2022.101781] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/19/2022] Open
Abstract
ClpP is a highly conserved serine protease that is a critical enzyme in maintaining protein homeostasis and is an important drug target in pathogenic bacteria and various cancers. In its functional form, ClpP is a self-compartmentalizing protease composed of two stacked heptameric rings that allow protein degradation to occur within the catalytic chamber. ATPase chaperones such as ClpX and ClpA are hexameric ATPases that form larger complexes with ClpP and are responsible for the selection and unfolding of protein substrates prior to their degradation by ClpP. Although individual structures of ClpP and ATPase chaperones have offered mechanistic insights into their function and regulation, their structures together as a complex have only been recently determined to high resolution. Here, we discuss the cryoelectron microscopy structures of ClpP-ATPase complexes and describe findings previously inaccessible from individual Clp structures, including how a hexameric ATPase and a tetradecameric ClpP protease work together in a functional complex. We then discuss the consensus mechanism for substrate unfolding and translocation derived from these structures, consider alternative mechanisms, and present their strengths and limitations. Finally, new insights into the allosteric control of ClpP gained from studies using small molecules and gain or loss-of-function mutations are explored. Overall, this review aims to underscore the multilayered regulation of ClpP that may present novel ideas for structure-based drug design.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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34
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Li J, Liu Z, Hong M, Sun C, Zhang T, Zhang H, Ju J, Ma J. Semi-Synthesis of Marine-Derived Ilamycin F Derivatives and Their Antitubercular Activities. Front Chem 2021; 9:774555. [PMID: 34778219 PMCID: PMC8586704 DOI: 10.3389/fchem.2021.774555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is still a global disease threatening people’s lives. With the emergence of multi-drug-resistant Mycobacterium tuberculosis the prevention and control of tuberculosis faces new challenges, and the burden of tuberculosis treatment is increasing among the world. Ilamycins are novel cyclopeptides with potent anti-TB activities, which have a unique target protein against M. tuberculosis and drug-resistant strains. Herein, ilamycin F, a major secondary metabolite isolated from the marine-derived mutant strain Streptomyces atratus SCSIO ZH16 ΔilaR, is used as a scaffold to semi-synthesize eighteen new ilamycin derivatives (ilamycin NJL1–NJL18, 1–18). Our study reveals that four of ilamycin NJLs (1, 6, 8, and 10) have slightly stronger anti-TB activities against Mtb H37Rv (minimum inhibitory concentration, 1.6–1.7 μM) compared with that of ilamycin F on day 14th, but obviously display more potent activities than ilamycin F on day 3rd, indicating anti-TB activities of these derivatives with fast-onset effect. In addition, cytotoxic assays show most ilamycin NJLs with low cytotoxicity except ilamycin NJL1 (1). These findings will promote the further exploration of structure-activity relationships for ilamycins and the development of anti-TB drugs.
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Affiliation(s)
- Jun Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhiyong Liu
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mingye Hong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, China
| | - Changli Sun
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Tianyu Zhang
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao, China
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35
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Perez Ortiz G, Sidda JD, de Los Santos ELC, Hubert CB, Barry SM. In vitro elucidation of the crucial but complex oxidative tailoring steps in rufomycin biosynthesis enables one pot conversion of rufomycin B to rufomycin C. Chem Commun (Camb) 2021; 57:11795-11798. [PMID: 34676855 PMCID: PMC8577248 DOI: 10.1039/d1cc04794a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimycobacterial peptides, rufomycins, have their antibiotic activity conferred by oxidative tailoring of the cyclic peptide. Here we elucidate the roles of cytochrome P450s RufS and RufM in regioselective epoxidation and alkyl oxidation respectively and demonstrate how RufM and RufS create a complex product profile dependent on redox partner availability. Finally, we report the in vitro one pot conversion of rufomycin B to rufomycin C.
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Affiliation(s)
- Gustavo Perez Ortiz
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
| | - John D Sidda
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
| | | | - Catherine B Hubert
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
| | - Sarah M Barry
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
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36
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Zhou B, Achanta PS, Shetye G, Chen SN, Lee H, Jin YY, Cheng J, Lee MJ, Suh JW, Cho S, Franzblau SG, Pauli GF, McAlpine JB. Rufomycins or Ilamycins: Naming Clarifications and Definitive Structural Assignments. JOURNAL OF NATURAL PRODUCTS 2021; 84:2644-2663. [PMID: 34628863 PMCID: PMC8865217 DOI: 10.1021/acs.jnatprod.1c00198] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rufomycin and ilamycin are synonymous for the same class of cyclopeptides, currently encompassing 33 structurally characterized isolates and 9 semisynthetic derivatives. Elucidation of new structures prioritized the consolidation of the names and established the structures of four diastereoisomeric rufomycins with a 2-piperidinone, named rufomycins 4-7, including full 1H/13C NMR assignments. The characteristic HSQC cross-peak for the CH-5, the hemiaminal carbon in amino acid #5, allows assignment of the stereocenters C-4 and C-5 within this ring. Semisynthetic derivatives (rufomycinSS 1, 2, and 3) were prepared from a rufomycins 4 and 6 mixture to validate the structural assignments. Based on the X-ray crystal structures of rufomycins 2 and 4, considering the NMR differences of rufomycins 7 vs 4-6 compared to rufomycinSS 1 vs 2 and 3, and taking into account that two major conformers, A and B, occur in both rufomycinSS 2 and 3, structural modeling was pursued. Collectively, this paper discusses the NMR spectroscopic differences of the stereoisomers and their possible 3D conformers and correlates these with the anti-Mycobacterium tuberculosis activity. In addition, a look at the history prioritizes names and numbering schemes for this group of antibiotics and leads to consolidated nomenclature for all currently known members, natural and semisynthetic derivatives, and serves to accommodate future discoveries.
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Affiliation(s)
- Bin Zhou
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Prabhakar S Achanta
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Hyun Lee
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ying-Yu Jin
- Man Bang Bio Co., Ltd., Subsidiary of Myongji University Technology Holdings Ltd., Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Jinhua Cheng
- Myongji Bioefficacy Research Center, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Mi-Jin Lee
- Myongji Bioefficacy Research Center, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Joo-Won Suh
- Myongji Bioefficacy Research Center, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Sanghyun Cho
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Guido F Pauli
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - James B McAlpine
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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37
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Kazmaier U, Junk L. Recent Developments on the Synthesis and Bioactivity of Ilamycins/Rufomycins and Cyclomarins, Marine Cyclopeptides That Demonstrate Anti-Malaria and Anti-Tuberculosis Activity. Mar Drugs 2021; 19:md19080446. [PMID: 34436284 PMCID: PMC8401383 DOI: 10.3390/md19080446] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 01/08/2023] Open
Abstract
Ilamycins/rufomycins and cyclomarins are marine cycloheptapeptides containing unusual amino acids. Produced by Streptomyces sp., these compounds show potent activity against a range of mycobacteria, including multidrug-resistant strains of Mycobacterium tuberculosis. The cyclomarins are also very potent inhibitors of Plasmodium falciparum. Biosynthetically the cyclopeptides are obtained via a heptamodular nonribosomal peptide synthetase (NRPS) that directly incorporates some of the nonproteinogenic amino acids. A wide range of derivatives can be obtained by fermentation, while bioengineering also allows the mutasynthesis of derivatives, especially cyclomarins. Other derivatives are accessible by semisynthesis or total syntheses, reported for both natural product classes. The anti-tuberculosis (anti-TB) activity results from the binding of the peptides to the N-terminal domain (NTD) of the bacterial protease-associated unfoldase ClpC1, causing cell death by the uncontrolled proteolytic activity of this enzyme. Diadenosine triphosphate hydrolase (PfAp3Aase) was found to be the active target of the cyclomarins in Plasmodia. SAR studies with natural and synthetic derivatives on ilamycins/rufomycins and cyclomarins indicate which parts of the molecules can be simplified or otherwise modified without losing activity for either target. This review examines all aspects of the research conducted in the syntheses of these interesting cyclopeptides.
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Affiliation(s)
- Uli Kazmaier
- Organic Chemistry, Saarland University, Campus Building C4.2, 66123 Saarbrücken, Germany;
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)—Helmholtz Centre for Infection Research (HZI), Campus Building E8 1, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-302-3409
| | - Lukas Junk
- Organic Chemistry, Saarland University, Campus Building C4.2, 66123 Saarbrücken, Germany;
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)—Helmholtz Centre for Infection Research (HZI), Campus Building E8 1, 66123 Saarbrücken, Germany
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In Vitro Profiling of Antitubercular Compounds by Rapid, Efficient, and Nondestructive Assays Using Autoluminescent Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:e0028221. [PMID: 34097493 PMCID: PMC8284454 DOI: 10.1128/aac.00282-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anti-infective drug discovery is greatly facilitated by the availability of in vitro assays that are more proficient at predicting the preclinical success of screening hits. Tuberculosis (TB) drug discovery is hindered by the relatively slow growth rate of Mycobacterium tuberculosis and the use of whole-cell-based in vitro assays that are inherently time-consuming, and for these reasons, rapid, noninvasive bioluminescence-based assays have been widely used in anti-TB drug discovery and development. In this study, in vitro assays that employ autoluminescent M. tuberculosis were optimized to determine MIC, minimum bactericidal concentration (MBC), time-kill curves, activity against macrophage internalized M. tuberculosis (90% effective concentration [EC90]), and postantibiotic effect (PAE) to provide rapid and dynamic biological information. Standardization of the luminescence-based MIC, MBC, time-kill, EC90, and PAE assays was accomplished by comparing results of established TB drugs and two ClpC1-targeting TB leads, ecumicin and rufomycin, to those obtained from conventional assays and/or to previous studies. Cumulatively, the use of the various streamlined luminescence-based in vitro assays has reduced the time for comprehensive in vitro profiling (MIC, MBC, time-kill, EC90, and PAE) by 2 months. The luminescence-based in vitro MBC and EC90 assays yield time and concentration-dependent kill information that can be used for pharmacokinetic-pharmacodynamic (PK-PD) modeling. The MBC and EC90 time-kill graphs revealed a significantly more rapid bactericidal activity for ecumicin than rufomycin. The PAEs of both ecumicin and rufomycin were comparable to that of the first-line TB drug rifampin. The optimization of several nondestructive, luminescence-based TB assays facilitates the in vitro profiling of TB drug leads in an efficient manner.
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39
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Han J, Liu X, Zhang L, Quinn RJ, Feng Y. Anti-mycobacterial natural products and mechanisms of action. Nat Prod Rep 2021; 39:77-89. [PMID: 34226909 DOI: 10.1039/d1np00011j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to June, 2020Tuberculosis (TB) continues to be a major disease with high mortality and morbidity globally. Drug resistance and long duration of treatment make antituberculosis drug discovery more challenging. In this review, we summarize recent advances on anti-TB natural products (NPs) and their potential molecular targets in cell wall synthesis, protein production, energy generation, nucleic acid synthesis and other emerging areas. We highlight compounds with activity against drug-resistant TB, and reveal several novel targets including Mtb biotin synthase, ATP synthase, 1,4-dihydroxy-2-naphthoate prenyltransferase and biofilms. These anti-TB NPs and their targets could facilitate target-based screening and accelerate TB drug discovery.
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Affiliation(s)
- Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
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40
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Li L, MacIntyre LW, Ali T, Russo R, Koirala B, Hernandez Y, Brady SF. Biosynthetic Interrogation of Soil Metagenomes Reveals Metamarin, an Uncommon Cyclomarin Congener with Activity against Mycobacterium tuberculosis. JOURNAL OF NATURAL PRODUCTS 2021; 84:1056-1066. [PMID: 33621083 PMCID: PMC8068612 DOI: 10.1021/acs.jnatprod.0c01104] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Indexed: 05/21/2023]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases. Unfortunately, the development of antibiotic resistance threatens our current therapeutic arsenal, which has necessitated the discovery and development of novel antibiotics against drug-resistant Mycobacterium tuberculosis (Mtb). Cyclomarin A and rufomycin I are structurally related cyclic heptapeptides assembled by nonribosomal peptide synthetases (NRPSs), which show potent anti-Mtb activity with a new cellular target, the caseinolytic protein ClpC1. An NRPS adenylation domain survey using DNA extracted from ∼2000 ecologically diverse soils found low cyclomarin/rufomycin biosynthetic diversity. In this survey, a family of cyclomarin/rufomycin-like biosynthetic gene clusters (BGC) that encode metamarin, an uncommon cyclomarin congener with potent activity against both Mtb H37Rv and multidrug-resistant Mtb clinical isolates was identified. Metamarin effectively inhibits Mtb growth in murine macrophages and increases the activities of ClpC1 ATPase and the associated ClpC1/P1/P2 protease complex, thus causing cell death by uncontrolled protein degradation.
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Affiliation(s)
- Lei Li
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Logan W. MacIntyre
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thahmina Ali
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Riccardo Russo
- Rutgers,
The State University of New Jersey, International Center for Public Health, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Bimal Koirala
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Yozen Hernandez
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Sean F. Brady
- Laboratory
of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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41
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Su C, Tuan NQ, Lee MJ, Zhang XY, Cheng JH, Jin YY, Zhao XQ, Suh JW. Enhanced Production of Active Ecumicin Component with Higher Antituberculosis Activity by the Rare Actinomycete Nonomuraea sp. MJM5123 Using a Novel Promoter-Engineering Strategy. ACS Synth Biol 2020; 9:3019-3029. [PMID: 32916055 DOI: 10.1021/acssynbio.0c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ecumicins are potent antituberculosis natural compounds produced by the rare actinomycete Nonomuraea sp. MJM5123. Here, we report an efficient genetic manipulation platform of this rare actinomycete. CRISPR/Cas9-based genome editing was achieved based on successful sporulation. Two genes in the ecumicin gene cluster were further investigated, ecuN and ecuE, which potentially encode a pretailoring cytochrome P450 hydroxylase and the core peptide synthase, respectively. Deletion of ecuN led to an enhanced ratio of the ecumicin compound EcuH16 relative to that of EcuH14, indicating that EcuN is indeed a P450 hydroxylase, and there is catalyzed hydroxylation at the C-3 position in unit12 phenylalanine to transform EcuH16 to the compound EcuH14. Furthermore, promoter engineering of ecuE by employing the strong promoter kasO*P was performed and optimized. We found that integrating the endogenous ribosome-binding site (RBS) of ecuE together with the RBS from kasO*P led to improved ecumicin production and resulted in a remarkably high EcuH16/EcuH14 ratio. Importantly, production of the more active component EcuH16 was considerably increased in the double RBSs engineered strain EPR1 compared to that in the wild-type strain, reaching 310 mg/L. At the same time, this production level was 2.3 times higher than that of the control strain EPA1 with only one RBS from kasO*P. To the best of our knowledge, this is the first report of genome editing and promoter engineering on the rare actinomycete Nonomuraea.
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Affiliation(s)
- Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Nguyen-Quang Tuan
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Mi-Jin Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Xia-Ying Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Jin-Hua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Ying-Yu Jin
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
- R&D Center, MANBANGBIO CO., LTD, Cheoingu, Yongin, Gyeonggi-Do 17058, Republic of Korea
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
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42
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Shetye GS, Franzblau SG, Cho S. New tuberculosis drug targets, their inhibitors, and potential therapeutic impact. Transl Res 2020; 220:68-97. [PMID: 32275897 DOI: 10.1016/j.trsl.2020.03.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 11/18/2022]
Abstract
The current tuberculosis (TB) predicament poses numerous challenges and therefore every incremental scientific work and all positive socio-political engagements, are steps taken in the right direction to eradicate TB. Progression of the late stage TB-drug pipeline into the clinics is an immediate deliverable of this global effort. At the same time, fueling basic research and pursuing early discovery work must be sustained to maintain a healthy TB-drug pipeline. This review encompasses a broad analysis of chemotherapeutic strategies that target the DNA replication, protein synthesis, cell wall biosynthesis, energy metabolism and proteolysis of Mycobacterium tuberculosis (Mtb). It includes a status check of the current TB-drug pipeline with a focus on the associated biology, emerging targets, and their promising chemical inhibitors. Potential synergies and/or gaps within or across different chemotherapeutic strategies are systematically reviewed as well.
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Affiliation(s)
- Gauri S Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.
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Wolf NM, Lee H, Zagal D, Nam JW, Oh DC, Lee H, Suh JW, Pauli GF, Cho S, Abad-Zapatero C. Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:458-471. [PMID: 32355042 PMCID: PMC7193532 DOI: 10.1107/s2059798320004027] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/22/2020] [Indexed: 11/10/2022]
Abstract
The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1-ClpP1-ClpP2 proteasome complex. The structure of the potent antituberculosis macrocyclic depsipeptide ecumicin complexed with the N-terminal domain of ClpC1 (ClpC1-NTD) is presented here. Crystals of the ClpC1-NTD-ecumicin complex were monoclinic (unit-cell parameters a = 80.0, b = 130.0, c = 112.0 Å, β = 90.07°; space group P21; 12 complexes per asymmetric unit) and diffracted to 2.5 Å resolution. The structure was solved by molecular replacement using the self-rotation function to resolve space-group ambiguities. The new structure of the ecumicin complex showed a unique 1:2 (target:ligand) stoichiometry exploiting the intramolecular dyad in the α-helical fold of the target N-terminal domain. The structure of the ecumicin complex unveiled extensive interactions in the uniquely extended N-terminus, a critical binding site for the known cyclopeptide complexes. This structure, in comparison with the previously reported rufomycin I complex, revealed unique features that could be relevant for understanding the mechanism of action of these potential antituberculosis drug leads. Comparison of the ecumicin complex and the ClpC1-NTD-L92S/L96P double-mutant structure with the available structures of rufomycin I and cyclomarin A complexes revealed a range of conformational changes available to this small N-terminal helical domain and the minor helical alterations involved in the antibiotic-resistance mechanism. The different modes of binding and structural alterations could be related to distinct modes of action.
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Affiliation(s)
- Nina M Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hyun Lee
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Daniel Zagal
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Joo Won Nam
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Dong Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Joo Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Guido F Pauli
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
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Zhou B, Shetye G, Yu Y, Santarsiero BD, Klein LL, Abad-Zapatero C, Wolf NM, Cheng J, Jin Y, Lee H, Suh JW, Lee H, Bisson J, McAlpine JB, Chen SN, Cho SH, Franzblau SG, Pauli GF. Antimycobacterial Rufomycin Analogues from Streptomyces atratus Strain MJM3502. JOURNAL OF NATURAL PRODUCTS 2020; 83:657-667. [PMID: 32031795 PMCID: PMC7384767 DOI: 10.1021/acs.jnatprod.9b01095] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study represents a systematic chemical and biological study of the rufomycin (RUF) class of cyclic heptapeptides, which our anti-TB drug discovery efforts have identified as potentially promising anti-TB agents that newly target the caseinolytic protein C1, ClpC1. Eight new RUF analogues, rufomycins NBZ1-NBZ8 (1-8), as well as five known peptides (9-13) were isolated and characterized from the Streptomyces atratus strain MJM3502. Advanced Marfey's and X-ray crystallographic analysis led to the assignment of the absolute configuration of the RUFs. Several isolates exhibited potent activity against both pathogens M. tuberculosis H37Rv and M. abscessus, paired with favorable selectivity (selectivity index >60), which collectively underscores the promise of the rufomycins as potential anti-TB drug leads.
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Affiliation(s)
- Bin Zhou
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Yang Yu
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Bernard D. Santarsiero
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Larry L. Klein
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Cele Abad-Zapatero
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Nina M. Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jinhua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yingyu Jin
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Hyun Lee
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Jonathan Bisson
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Sang-Hyun Cho
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
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Yathursan S, Wiles S, Read H, Sarojini V. A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity. J Pept Sci 2019; 25:e3213. [PMID: 31515916 DOI: 10.1002/psc.3213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.
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Affiliation(s)
- Sutharsana Yathursan
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Hannah Read
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140, New Zealand
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46
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Strategies in anti-Mycobacterium tuberculosis drug discovery based on phenotypic screening. J Antibiot (Tokyo) 2019; 72:719-728. [PMID: 31292530 PMCID: PMC6760628 DOI: 10.1038/s41429-019-0205-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 11/20/2022]
Abstract
The rise of multi- and extensively drug-resistant Mycobacterium tuberculosis (M. tb) strains and co-infection with human immunodeficiency virus has escalated the need for new anti-M. tb drugs. Numerous challenges associated with the M. tb, in particular slow growth and pathogenicity level 3, discouraged use of this organism in past primary screening efforts. From current knowledge of the physiology and drug susceptibility of mycobacteria in general and M. tb specifically, it can be assumed that many potentially useful drug leads were missed by failing to screen directly against this pathogen. This review discusses recent high-throughput phenotypic screening strategies for anti-M. tb drug discovery. Emphasis is placed on prioritization of hits, including their extensive biological and chemical profiling, as well as the development status of promising drug candidates discovered with phenotypic screening.
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